Contacts of the strand formed by residues 181 - 188 (chain B) in PDB entry 1PZY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 181 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B SER 4.8 9.0 - - - +
179B PRO* 3.6 2.2 + - - +
180B HIS* 1.3 71.4 - - - +
182B VAL* 1.3 58.9 + - - +
212B ASP* 3.3 16.2 - - + +
243B TYR* 3.8 30.1 - - + -
244B ASP* 3.0 41.0 + - - +
245B TYR* 3.4 11.6 - - - +
246B ASN* 2.9 51.6 + - + +
247B CYS 3.1 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B HIS* 3.7 26.2 - - + +
181B LYS* 1.3 74.5 - - - +
183B ALA* 1.3 69.0 + - - +
184B ILE* 4.0 8.7 - - + -
211B LEU* 4.5 7.4 - - + -
212B ASP 2.8 8.9 + - - -
213B TYR* 3.0 18.4 - - + +
214B GLY 3.0 24.3 + - - -
245B TYR* 3.4 6.0 - - - -
247B CYS* 3.3 22.9 - - + +
249B VAL* 3.7 30.1 - - + +
264B TYR 3.9 16.2 - - - +
265B ARG* 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 1.3 71.9 - - - +
184B ILE* 1.3 61.3 + - - +
185B ILE* 3.1 9.4 - - + +
214B GLY 3.7 5.2 - - - -
216B TYR* 4.2 2.9 - - + -
239B ALA* 3.9 12.6 - - + -
245B TYR* 3.5 32.6 - - + -
247B CYS 2.9 6.9 + - - -
248B PHE* 3.3 21.7 - - + -
249B VAL 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 4.0 17.3 - - + +
183B ALA* 1.3 72.0 - - - +
185B ILE* 1.3 60.8 + - - +
186B ILE* 3.9 8.6 + - + +
198B TRP* 3.7 27.6 - - + -
206B LEU* 3.4 45.5 - - + -
211B LEU* 5.6 0.2 - - + -
213B TYR* 4.7 7.6 - - + -
214B GLY 3.0 14.7 + - - +
215B ILE* 3.7 9.1 - - + -
216B TYR* 2.9 29.5 + - - +
249B VAL* 3.3 21.5 - - + +
251B SER* 4.7 4.5 - - - -
264B TYR* 4.4 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ALA* 3.1 27.8 - - + +
184B ILE* 1.3 71.2 - - - +
186B ILE* 1.3 64.8 + - - +
187B PRO* 3.9 2.6 - - - +
216B TYR* 3.5 7.6 - - + -
218B ILE* 3.7 25.1 - - + -
232B LEU* 3.8 23.7 - - + +
235B GLY* 3.8 27.4 - - - +
236B PHE 4.2 1.1 - - - +
248B PHE* 3.7 27.8 - - + -
249B VAL 2.8 12.9 + - - +
250B PHE* 3.4 17.2 - - + -
251B SER* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE* 4.5 5.6 - - + +
185B ILE* 1.3 80.8 - - - +
187B PRO* 1.4 75.5 - - - +
188B PHE* 3.5 4.7 + - + +
195B LEU* 4.7 4.0 - - + -
198B TRP* 3.8 52.3 - - + +
215B ILE* 4.4 5.8 - - + -
216B TYR 2.9 13.5 + - - +
217B VAL* 3.6 22.5 - - + -
218B ILE 3.0 24.0 + - - -
251B SER 3.3 16.8 - - - +
253B VAL* 3.7 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 1.4 87.6 - - - +
188B PHE* 1.3 60.5 + - - +
218B ILE* 3.9 4.7 - - + +
226B PHE* 3.9 16.6 - - + -
228B ARG* 4.0 29.8 - - + +
231B LEU* 4.3 10.8 - - + -
232B LEU* 3.6 20.3 - - + -
251B SER 3.2 15.3 - - - +
252B ASP* 4.0 14.1 - - - +
253B VAL* 4.7 0.2 - - - +
407B UDP 3.0 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 3.8 1.3 - - + +
187B PRO* 1.3 76.6 - - - +
189B ARG* 1.3 74.8 + - - +
190B ASN* 3.6 12.1 - - - -
191B ARG* 3.4 45.8 - - + -
192B GLN* 3.8 21.5 - - + -
195B LEU* 4.3 17.7 - - + -
217B VAL* 3.4 30.1 - - + -
218B ILE 2.9 12.1 + - - +
219B ASN* 3.2 24.6 - - - -
220B GLN* 2.9 27.7 + - - +
226B PHE* 3.8 10.2 - - - -
231B LEU* 4.2 0.4 - - - +
253B VAL* 4.6 7.6 - - + -
393B LYS* 4.0 18.2 - - - -
407B UDP 3.3 7.0 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il